rs1522889

Variant names:

• chrX-121390334-C-A
• rs1522889

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.428 in 110,717 control chromosomes in the GnomAD database, including 7,785 homozygotes. There are 13,567 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (7785 hom., 13567 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 47321 AN: 110663 Hom.: 7788 Cov.: 22

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.451

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.428 AC: 47337 AN: 110717 Hom.: 7785 Cov.: 22 AF XY: 0.411 AC XY: 13567 AN XY: 33013

African (AFR) AF: 0.386 AC: 11746 AN: 30392

American (AMR) AF: 0.327 AC: 3438 AN: 10517

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 1496 AN: 2639

East Asian (EAS) AF: 0.0133 AC: 47 AN: 3525

South Asian (SAS) AF: 0.362 AC: 952 AN: 2628

European-Finnish (FIN) AF: 0.414 AC: 2424 AN: 5852

Middle Eastern (MID) AF: 0.542 AC: 115 AN: 212

European-Non Finnish (NFE) AF: 0.497 AC: 26207 AN: 52781

Other (OTH) AF: 0.450 AC: 676 AN: 1503

Alfa AF: 0.470 Hom.: 12646

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.66
PhyloP100		-0.19

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1522889; hg19: chrX-120524188;